During the last year, we have optimized the conditions to purify protein complexes using antibody against FLAG-tag from mouse ES cells. We used mouse ES cells, where a FLAG-tagged transcription factor can be overexpressed in the absence of tetracycline for 72 hours. The purified protein complex was first analyzed by silver-stained gels and subsequently analyzed by mass spectrophotometry. The results indicate that our procedure works well. We are currently scaling up the procedure to analyze protein complexes for the initial 60 TFs. To aid in the protein complex analysis, we have also developed a database of mouse protein-protein interactions by transferring the protein-protein interaction information experimentally obtained from other model organisms.